1998 Ford Expedition

Engine Performance problem
1998 Ford Expedition V8 Four Wheel Drive Automatic 98000 miles

i have a 1998 ford expedition xlt, a couple months back my engine started running a little rough, and idled a little rough too, the check engine light came on, I took it to autozone and they said that the left side of my engine was not running efficient. The check engine light stayed on but a couple days later the roughness went away. It felt like I have lost some power that came back every now and then. Just the other day it started riding rough again with acceleration and at an idle, but in neutral there is no roughness that I can tell of. I have no idea what it could be or what direction I should head in, any advice would be greatly appreciated.
April 2, 2009.

What code did AZ get? Also, when was the last tune up? Finally, which size engine do you have?